First: I downloaded the "Tropical" mod from here: http://www.moo3.at/mods/ - If there is a later/better version of tropical, I'd love to hear about it - I just literally got to doing this this morning and didn't poke around too hard to find the mods. Presumably this also works with "Strawberry" and "Vanilla" as well. I'm currently not vouching for the quality of the patches as I am just checking them out myself, but how to get them installed.
WARNING: the only thing that WILL NOT WORK is windowed mode. There's nothing currently that can be done about this unfortunately as windowed mode runs in some kind of weird 16-bit mode that does not play nice with 64-bit windows. This is literally the only problem.
#0: Download Moo3 from Gog and the mod of your choice from the mod site, above.
#1: Install Moo3.
#2: Back it up! Just copy the whole install directory and paste it right back into the gog directory. It'll back up everything into "Master of Orion 3 - Copy" - this is much easier to restore than from the install.
#3: Extract the mod package to its own directory and DELETE moo3.exe - we won't be using it, but rather the GOG (drm-free) moo3.exe. THIS IS IMPORTANT. If you don't delete the pre-modded executable you will be starting over.
#4: Copy the contents of the mod directory into your Moo3 directory. All of it. Make sure you click "yes" to the copy confirmation and to REPLACE the original files.
#5: Run Moo3Patcher.exe - this is what will apply the patches to the GOG moo3.exe.
- this next step is critical -
#6: Underneith the patch window is a window That says "Moo3DLL.dll" - there's an install button next to it. press it. If it can't find the file, browse to the Moo3DLL.dll file in the moo3 directory. This is from the mod files. You want this.
#7: Some tedium: You have to manually patch in all the patches you want in the window above - just click on it and hit 'patch'. If it is successful, it'll say so in the status column. If it's not successful, make sure you did step 6 (only an issue for the ones that say "Yes" in the dll column), and that in the bottom window it's pointing to the Moo3.exe file to patch. There must be a typo in the patcher database because on one patch (forget which) this has an extra "\" in the directory string and it needs to be re-pointed to the Moo3.exe file.
#8: Apparently patching in SenateVictory breaks Allied Victory, and vice-versa. if you patched in AV first. You just need to "unpatch" Allied victory, and then "repatch" it. Oh well. Pick one.
#9: DO NOT PATCH IN WINDOWED MODE. Don't say I didn't warn you.
If you follow/ my instructions you should be able to get every patch in with the exception of the SV/AV which are exclusive for some reason.